well this is a general way to approach a fight with any class, but the key is to always be aware of what the other person is trying to do to you.
with a hunter once you get to them, odds are they are going to drop a trap then disengage, so as a rogue you want to think about how to "counter" these tactics. for traps, you can vanish bug or trinket freezing traps, and in 3.1 the same for frost traps, but theres more you can do than that.
if you have a hunter in a cs, when its about to end you know the hunter is most likely going to do some combination of trap/disengage (btw you should probably dismantle toward the end of cs so they cant simply disengage conc shot), so first of all, just like running away from priests at the end of a cs to try to get them to waste their fear, you can move away from a hunter so they cant drop a trap on you and have it set off immediately(with frost traps, its worth almost anything to avoid setting them off).
next is the disengage. put yourself in a hunters perspective... odds are youre freaking out because a rogue is on you and thats not good, so youre trying to get your trap down then gtfo, so basically you know the hunter is going to disengage as soon after the trap as they can, so try to predict the disengage with a gouge... that way you can back on to the hunter without them being able to run away or even shoot at you if they arent already dismantled. also something to keep in mind is that a good hunter will probably be aware of the terrain before disengaging, so if you fight a hunter that does that, wait for them to position themselves so they arent going to disengage into a hill 2 inches away, then gouge.
so if that all goes well you are on the hunter and they have a long disengage/trap cooldown so you should probably be able to kill them or get close (if not make sure you get bleeds up for the next trap/disengage set so they cant get away and bandage). also note that rng sucks so when you get to the hunter after the disengage, when dismantle ends or immediately if it wasnt up at all, pop evasion to avoid them wing clipping you and getting away because of some fluke poison proc drought. (against dward hunters you should save evasion for when they stoneform i think).
the best tip i can give you for this situation though: play swords! ive played 29 rogues for a long time, with a decent mix of all specs, and now i only play combat swords, because imp sprint, imp gouge, and endurance make hunters sooo much easier to deal with, and ive found that rogues really dont have much trouble with other classes (except priests, not for long with the mana regen change though) so losing those big dagger crits in exchange for being able to deal with hunters is a trade off well worth making.
and something i left out in this post is what to do when the hunter uses their longer cds, i.e. trinket/stoneform. and really, i dont know. i havent found a pattern consistent enough in hunter trinket/stoneform useage to really make a general strategy in dealing with them. in general though, try to have evasion when the hunter stoneforms, because if theyre on top of you itd be bad if they wing clipped you and got away. if you can, save your gouge for the stoneform, since its best for the hunter to be sitting in a gouge while the stoneform duration ticks away. so i guess you have to think quickly when the stoneform comes, first trying to gouge, then popping evasion either at the end of the gouge or as soon as you know you cant gouge them (i.e. its on cd or it doesnt land).
with the pvp trinket, all you can really do is try to be aware, because its really not that useful if you are paying attention. a hunter can potentially use it to break out of a cs/gouge/poison... all of which they are probably in because you are on top of them, so just be ready for the trinket, then get a poison back on them right after. if you notice a pattern in how the hunter uses their trinket, then save energy for when they are going to use it, and either gouge, or use a special to increase the chance of getting a poison back up as soon as they use the trinket (not too soon though, they get 1 second immunity to cc/slows after using it i think?).
and i saw someone mention nature resistance too, which i saw a good amount of on cyclone because people frequently used 15 nr to cape to get resistance to poisons/roots/purges. as far as i know, nature resistance no longer effects the chance of these landing. im "pretty sure" that when spells were made so that they "miss" rather than "resist" they became immune to the effects of resistances. so i think binary spells (i.e. spells that eiter hit or miss) like poisons will have a proc rate unaffected by spell resistances, although poisons like any spell have a base resist chance (another good reason to go swords =) ). im not really to sure about that last paragraph though, so itd be cool if someone could confirm/deny that with actual proof.
